Guilty Until Proven Innocent
by Ashley5627
Summary: Neal wakes up to find himself arrested for a murder he did not commit. With all evidence pointing towards him and the police harboring a personal vendetta against him, can he rely on Peter to get him out? Or will go to jail for something he didn't do? Neal!Whump
1. Wake up call

**AN: this is my first story so please be kind! **

**I would like to give a huge thank you to ****XXAlmostInsaneXX for beta-ing my story to help make a lot better! **

**Also I would love feedback. Thank you for reading!**

**Disclaimer: I do not own White Collar, I'm just borrowing them.**

It was 11 pm on a Friday and Neal just turned in for the night. He had had a long week at the office and just wanted to sleep.

He was just about to fall asleep when he heard knocking – no, pounding on the door, and if he could hear it from his room then it was really loud.

June was at her granddaughter's house for the weekend and the staff was off as well.

So he knew the non stop pounding on the front door will go unanswered if he didn't get up and see who it was. He was just about to get up and answer it but it suddenly stopped, So He thought they just left.

Then out of nowhere there was a huge bang and he bolted upright in his bed. He could hear footsteps coming up the stairs to his apartment, a lot of them – and _wow_, these people were loud. He got out of bed and thought about running for a second then he thought 'why would anyone bother knocking on the door if they wanted to kill or kidnap him? Maybe they were cops?'

That thought made him want to run even more, but hadn't done anything wrong… at least not recently – nothing that they could prove anyway. So he decided to stand his ground, in nothing but his maroon pyjama bottoms, Neal suddenly felt vulnerable.

Neal walked over by the door, far enough away to not get hit by the door if they knocked it down. And then, just like he thought, the door was busted down and five SWAT team members came rushing in "NYPD! Hands in the air! Don't move!" They seemed to yell all at once.

Neal had his hands in the air before they Finished there first sentence – he had done this before, once or maybe twice. There was five very large guns pointed at him and he knew to listen to the people that were holding them.

A sixth man walked through the door, or where the door should have been. He was wearing a cheap suit and Neal knew he was in charged by the way he looked and walked, there was just an air about him that seemed to say that he got his way. He addressed Neal, "Neal Caffery?"

"Yes?" Neal replied hesitantly.

"My name is Detective Brooks, you're under arrest," he said. He looked angry.

"What? On what charges?" Neal said.

"For the murder of Officer Frank Downs," Brooks said like as if Neal should have known. He got out his handcuffs and started walking towards Neal.

"Murder!? I didn't kill anyone!" Neal cried, confused. He would never kill anyone. Steal priceless paintings? Yeah – that might be something he could get arrested for, if anything. But murder? Never.

"Yeah, that's what they all say." And wasn't that the most cliché thing the police officer could have said.

"Wait! Can I at least put a shirt on?" Neal asked. He will get this figured out at the station, but right now he wanted a shirt.

"You gave up that right when you killed one of our own!" Brooks growled and punched Neal in the stomach. Neal fell to his knees and coughed, trying to get his breath back and control the pain. Then Brooks grabbed Neal's hair and pulled so he was looking at him. "We take it personally when someone like you kills one of our own," he hissed at him.

"I – I can see that but I'm afraid you have the wrong guy. I didn't-" Neal tried to explain but was cut off by a blow to the face, Brooks let him go and he fell backwards onto his back. Then he was kicked in the side. Neal couldn't help the whimper that escaped and he curled around himself. One more kick in the stomach knocked all the breath out of him and a bot in the back was enough to bring tears to his eyes.

"You little bastard! You're not worth the air you breathe!" the detective yelled.

He then turned Neal so he was facing the floor and pulled his hands behind his back, cuffing his wrists and tightened them till they dug into his skin. Neal sucked in a sharp breath. Since the last time Neal talked he was attacked, he chose not to comment or plead his case anymore. He had a feeling they won't listen.

Neal has had his fair share of arrests but he was never attacked like this. 'I think this is police brutality,' Neal thought as he was dragged to his feet and pushed out of the door and taken to the waiting police cruiser. Brooks slammed Neal's head against the car while leading him in.

"Oops," he said. Neal didn't think he meant it.

Neal was dazed for a few moments, swallowing a few times to help the sudden nausea. He heard the door close and the two front ones open and close, then they were off to the station, where he hoped there were more reasonable cops.

Most of the ride Neal was laying on his side trying not to think of the pain and the danger he was in and try to come up with a plan. 'I can't go to jail for something I didn't do right?' Neal thought.

In the end his worst plan was to pick the cuffs and jump out of the car – not very fun and very painful given his state – and his best was to ask, very nicely, for a phone call, to call Peter and ask him, also very nicely, to get his butt out of jail, please. Yeah that sounded more like a plan.

After many sharp turns - either this guy doesn't know how to drive or he was doing it on purpose- they made it to... somewhere. Neal wasn't sure, he was still lying on his side.

The cars engine turned off and the two officers got out. Neal was struggling to sit up, but the pain in his ribs didn't help and neither did the nausea. The 'boys in blue' opened the back door and 'helped' Neal out, none too gently. Still in just pyjama bottoms, Neal really felt the cold November wind bite his skin.

The lovely gentlemen who helped him out of the car shoved him into the back door of the station. 'The back door? Why the back door? And why did no one read me my rights?' Neal thought. They proceeded to haul Neal to a small room in the basement. It was not big, maybe ten feet by ten feet. It had a metal table and two metal chairs, but it did not look like a normal interrogation room. This did not look good.

The two nice escorts sat him in the chair at the table that was facing the door, secured the handcuffs to the chair, and started to leave, but Neal stopped them. "Can I get my phone call now?" The bigger, and scarier looking one, did not like that Neal had spoken, so he punched him in the face. Neal's head snapped to the side and he saw stars for a second.

"No," Mr. Big and scary said, and left.

So that left Neal alone and confused. 'Why do they think I killed someone? Why am I not in a real interrogation room? And why do they have to hit me every time I talked?'

He had a lot of questions and no answers.

In the quiet room Neal heard a faint beeping sound, and he look around. It took him a moment to realize it was coming from him – no, from his anklet. The anklet! He was out of range. Why had he not thought of that before? He must have hit his head harder than he thought. Peter should be here any minute now. All Neal had to do was wait.

Neal did wait, and then waited some more. He didn't know how much time went by, but Peter should have been here by now, right?

The room was cold. Colder than it had seemed to be a few minutes ago. His head really hurt, and his abdomen, and his wrists. He was not having a good day.

After what seemed like forever, the door opened only for Brooks to walk in again. Great.

He came up to the table and pulled out the other chair, it dragged along the floor and Neal winced, the harsh sound like daggers to his head.

He sat down and opened up the file he had brought with him. He took out some pictures and put them in front of Neal.

They were of a dead body, a bullet hole in his head and blood going down the side of his face. It look like it was done execution style. They made Neal's stomach roll and he swallowed convulsively and look away.

Brooks was just starting at him with dead eyes. It really creeped Neal out.

Then Neal did something he regretted. He opened his mouth.

"I didn't kill him. I didn't kill anyone."

"Bullshut!" Brooks said, and Neal could feel the spit on his face. "We have your fingerprints on the murder weapon and at the crime scene."

Damn. That's not good. "I didn't kill him. I don't even know who he is!"

And Neal guessed that was the wrong thing to say, because Brooks grabbed Neal's hair – again – and made him look at the pictures. Neal tried to pull away, but Brooks was too strong and Neal couldn't use his hands. Another glance at the pictures sent Neal over the edge. That and the pounding in his head and he threw up just as Brooks moved away. Man, he wished he could have thrown up on Brooks.

Brooks was cursing and yelling as Neal emptied his stomach. He went to the door and open it up. "Damn it! Riggs get in here and clean this up!" Brooks said, then left.

Neal had stopped puking and was just breathing through his mouth so he didn't have to smell the mess. Someone opened the door and came in. He was dressed in a police officer uniform and looked like he was just out of the academy. He was holding a bucket and a rag. He refused to look at Neal and went to work on the mess.

Neal thought that maybe he could reason with him. "Hey, do you think you could get me a shirt or something? Maybe turn up the heat? It's kind of cold in here."

Riggs just looked up at him for a second then finished cleaning up the mess. He was just about to get up when he heard the beeping of the anklet. He looked surprised that it was there. "What is this?" Riggs said.

"It's a tracking anklet." Duh.

Riggs got up, picked up the bucket and left. Probably to tell on him.

About five minutes later, give or take, the door opened and Brooks came in again. He sat at the table and asked, "Why do you have a tracking anklet?" In an even voice.

Neal knew he shouldn't, but he did. "It's a fashion accessory of course. It's all the rage right now," he said, with a big smile on his face that he did not feel. Not a good idea.

Brooks came around to Neal faster than he thought he could and slammed his face on the table, hard. The pain in Neal's head doubled, the movement pulling at the handcuffs, and they dug into his wrists. Neal hung his head and tried to control his pain, anger and nausea. He was getting really sick of dumb cops beating him up.

He saw blood dripping onto the pictures on the table. His nose is bleeding. Great.

"You're a little smartass aren't you?"

'Smarter than you.' The retort was on the tip of Neal's tongue, but he did not want to get 'punished' again. 'I guess he forgot about his first question.' Neal thought.

Neal opened his eyes and saw the damage that was done to his chest and stomach. The left side of his stomach was red and turning purple-ish, so was his chest. He did not want to see what his back, wrists and face looked like.

"So now you're not talking to me?" Brooks sneered. "Got nothing to say now, smart mouth?"

Neal was confused, was his ass smart or was it his mouth? Or was it both? He did not think Brooks would understand the humor in that, so he instead said "Can I just call someone please? He will sort this all out."

Apparently Brooks did not care if Neal said please or not. Still looming over Neal, Brooks punched him in the chest, then again. Neal could have sworn that he felt something snap. He doubled over as much as he could with the restraints, and coughed. "You don't get it do you? You will not get a phone call, you will not get a shirt, and you will only get to talk if you are confessing to the murder you committed," Brooks snarled.

Neal thought he would try one more time, so he looked Brooks straight in the eyes and said "I did not kill anyone." Slow enough that maybe he would understand. Judging by the fist that hit Neal in the face, he did not.

"When you're ready to confess, let me know," Brooks said. Then he walked to the door and Neal caught a glimpse of his watch, 1:38. Peter had to have been here by now if he had been informed that Neal was out of range. Right? Maybe he was here, but they weren't letting him see Neal.

After a few minutes of thinking, Neal got bored. And with nothing to distract him, his thoughts went to his injures. His head, chest, stomach, wrists, and back all seem to throb with every heartbeat. And the more he thought of them the more they hurt. At least his nose had stopped bleeding.

Trying to stop thinking about the pain, he let his mind drift, and after a while he passed out, thinking 'Peter, please find me.'

Peter

Peter arrived at June's mansion at 9:26 am. Since Neal had worked so hard all week, Peter thought that Neal deserved a reward. So today Peter was going to take him to the MET. And since June was gone for the weekend he thought Neal might be a little lonely in this big house all alone.

He got out of his Taurus and made his way to the front door. Once he was a few feet from the door, he saw that it was slightly ajar. His hand automatically going to his gun, Peter approached the entrance.

He saw that the lock was broken. He drew his weapon and quietly pushed the door open. He went through each room systematically, even though he wanted to run up the stairs to Neal's room and just make sure he was okay. But the FBI agent in him knew that he couldn't.

So after the first two floors, Peter made it up to Neal's room. He saw the door on the floor and walked over it and into the apartment. "Neal?" Peter called out. There was no answer. He looked around and saw blood on the floor. Damn. He finished clearing the room and came back to the blood on the floor. In was only a few drops, but it was blood and it was dry.

Peter pulled out his phone and called Neal's cell. After a few seconds he could hear ringing in the apartment and he looked to see Neal's phone on his nightstand.

Peter ended the call, then pulled up his tracking data on his phone. It said he was here.

"Neal?" He tried again. Nothing.

After a few more minutes of looking around, Peter gave up and called Diana. She was working today and he knew she would help figure this out.

**Ok! That was chapter one! Please tell me what you think! Thank you!**


	2. A little worse for wear

Neal

Neal woke with a start, and looked around. Oh yeah, the small room in the police station. With the memories, the pain came as well. His whole body ached from the beatings and the position he had forced to be in.

He would have been out of the handcuffs in seconds if he was wearing one of his suits. He always had lock picks in the seams. And it was still cold in here, so having a little more clothes would be nice too.

After a while, the door opened again and Brooks came in again. Neal was really hoping to see the 'good cop' soon.

Brooks took his seat again and said "You have four hours to confess or we will just throw you in a cell and take this to court later. Your choice."

"What time is it?" Neal asked.

Brooks thought for a second, then decided that giving that information wouldn't hurt. "8:47," he said blankly.

8:47. Peter will be here any time now. All Neal will have to do is wait. "I'm not confessing to something I didn't do," Neal said.

"We have your fingerprints. You're going to jail one way or another," Brooks said, and then looked down at the pictures on the table. Sadness and then anger flashed across his face. He looked up at Neal. The latter seemed to be directed at him. "You killed Frank and you will not get away with it," Brooks growled.

"I was framed. I didn't kill him. Call agent Peter Burke of the FBI. He will tell you-" The anklet! "Do you have a time of death? When did he die?" Neal asked.

Brooks did not seem happy about the question, but said "Friday, from six to eight at night."

Friday night. Peter was with him. They were on a stakeout. In the van. And Neal had had his tracker on! He had an alibi! "This tracker on my ankle will prove I did not kill anyone. And someone was with me all Friday. His name is Peter Burke. He's my handler."

Brooks thought about that for a minute. He still looked mad. "Why do you have a tracking anklet?"

Back to this question. "I'm on a work release program. I help out the Feds, and they keep me out of jail," Neal hoped that was a simple enough for Brooks to understand.

He seemed to understand. "What's your handler's name again?"

"Agent Peter Burke," Neal gave Brooks his cell number and Brooks left to call him. Neal let out a sigh of relief. He was finally getting somewhere.

After maybe ten minutes, Riggs came in again, holding an old looking black t-shirt. "Mr Caffery?" He said. Neal nodded. "Brooks said you wanted a shirt?"

Finally, good cop. "Yes, yes I did."

Riggs came over and unlocked the cuffs. Neal brought his hands around slowly and rubbed his wrists. He look at them and grimaced. They were red and purple. At least the cuffs didn't break skin. Then Riggs gave him the shirt, and Neal put it on, wincing when it aggravated his many aches and pains. It's smelled faintly like body odor, but it was a shirt.

Riggs looked at Neal apologetically "Can you stand up please?" Neal got up and a wave of dizziness came over him and gripped the table. After a moment, it passed and Riggs put the cuffs back on, about as tight as they were and he grabbed Neal by the elbow and led him out of the room, up some stairs and to a room that did look like an interrogation room. This one had three chairs around a table and it had a two-way mirror. Riggs sat him in a chair and cuffed him to the chair in the same manner as before, then he left.

A few minutes later, Brooks came in again and sat down. Looking Neal right in the eyes he said in a deadly voice, "You resisted arrest. We had to restrain you, but you put up a fight, and you took a few blows. Simple as that. Think you can remember that? Or do you – and your friend, Burke – need to be persuaded?" Neal swallowed nervously. He did not want to be persuaded. And he would never let anyone he cared about get hurt.

"N-no. No need. I'm sure I can remember," Neal said.

Brooks nodded. "Good." He said and got up faster than Neal expected and he flinched a little. Brooks smirked and left.

What was he going to do? He was going to tell Peter what happened, but now he couldn't say anything. He won't let Peter get hurt.

So now all he had to do was wait. But Neal was not feeling good. His...everything hurt and he was tired. So he let his head droop and fell into a restless sleep.

Peter

After hours of searching, Peter still has no idea where Neal was, and he was really starting to get worried. The Marshals still don't know what was wrong with Neal's tracking data, because Neal was definitely not at June's. And they hadn't gotten the test results back, but it's the same blood type as Neal's.

So now Peter was in his office waiting for Mozzie to call him back after he had left a few messages on his phone and going through the last case they were on to see if someone wanted to hurt Neal for help locking them up.

Suddenly his cell went off and he answered. "Hello?" he said.

"Is this Peter Burke?" someone on the other end said.

"Yes. Who is this?"

"Do you know a Neal Caffery?" the voice on the other end asked.

"Yes. Why? Do you know where he is?"

"I think you should come down to the 11th precinct. We need to ask you a few questions about him. He says you were with him Friday night."

"He's down there?" Peter asked.

"Yes. Can you come down here?" Neal got arrested? At least he's not dead in a ditch.

"I'll be there in 20 minutes," Peter confirmed and hung up. He then quickly updated Diana and Jones. Then he made his way to see Neal.

When Peter made it to the police station he realized that he didn't know the name of the man that talked to him on the phone. So he made his way to the front desk. "Agent Peter Burke," he said automatically and flashed his badge. "I'm here for Neal Caffery," he said to the middle aged woman at the desk.

She looked him up and down and said "Come with me." She led Peter through the station to a man in a suit at a desk. "Mr Burke, this is Detective Myers, he's in charged of the Downs case," she said and left them.

"Where's Caffery?" Peter said before Myers could say anything.

"Right this way," Myers said and led Peter down some hallways and to a door, but didn't open it right away. "Mr Caffery resisted arrest when we brought him in so he may look a little roughed up," Myers warned. Peter frowned. There was no way in hell that had happened. Neal Caffery never resisted arrest, preferring instead to talk his way out of any situation.

Peter just pushed past him and opened the door, and walked in with Myers following. He saw Neal sitting at a table and when he looked up at him, Peter could see a bruise on his face as well as dried blood from his nose and a cut on his lip.

"Peter," Neal said and smiled at him. Peter could hear the relief in his voice.

"Are you okay?" Peter asked. Neal nodded slowly. Now that Peter knew that Neal was safe, his worry turned to anger. "Neal why were you arrested?" Peter asked next, maybe a little too harshly, because Neal's smile faltered and he looked confused.

"They didn't tell you?" Neal said slowly.

"No. I just got here." Then Peter looked at Myers for answers.

"We arrested Caffery for murder," Myers said.

"Murder?" Peter said and laughed. Neal wouldn't kill anyone. But by the lack of laughter, this was no joking matter. "Neal didn't kill anyone." Peter said in a matter of fact tone.

But Myers didn't look convinced. "Why do you think Neal killed someone?" Peter asked the detective instead.

"His prints were on the murder weapon and at the crime scene," Myers said.

"I didn't kill anyone," Neal slurred. Peter bet that that had been his mantra this whole time here.

"I know, Neal." Peter told Neal. He then turned to the detective. "When was the murder committed?"

"Last Friday night," Myers said.

"He was with my all Friday. He didn't kill anyone." Peter told Myers and looked over at Neal. He looked half awake. He walked over to Neal and lifted his head by his chin. His pupils looked dilated and unfocused. "Neal?" Peter said.

It took a second for Neal to focus on him. "Hmm?" Neal said.

"Did you hit you head?"

"Yes." He said after a moment.

Peter let Neal's chin go turned to Myers. "Has he been looked at? I think he has a concussion," Peter said, trying not to get mad.

"Uh, no," Myers said.

Peter looked back at Neal and saw his head on his chest and his eyes closed. "Neal?" Peter said and picked up his chin again. "Neal? You okay?" He didn't open his eyes. Peter tried tapping he cheek. Nothing. "Neal!" He almost yelled. "Get me an ambulance! Now!" He said to Myers, who left the room in a hurry.

"Neal, come on wake up for me, please."

Neal's eyes finally opened. "P'ter? Hurts," Neal slurred.

"What hurts buddy?"

"Head, chest," Neal said

"I'm going to lift up your shirt, okay?" Peter said. Neal mumbled something that sound like 'okay' so let go of Neal's chin and his head drooped a bit. Then Peter carefully pulled up the old t-shirt and Neal sucked in a sharp breath. Peter could see why, his chest and abdomen were covered in an array of red, blue and purple bruises. Peter pulled down the shirt again. "You're going to be okay Neal. We're going to patch you up," Peter told Neal and patted him on the shoulder softly.

He walked around the chair and pulled out his handcuff key from his pocket and unlocked the cuffs while holding Neal's chest so he won't fall forward. Neal's wrists were bruised and looked horribly painful. Peter came around and switched his hold to Neal's shoulders and crouched down in front of him. Peter could see the lines of pain on his face. "What happened Neal?"

"Asked for a shirt," Neal laughed bitterly and winced. "At least I got one 'ventually. Smells though," Neal said and made a face.

A shirt? Neal must be really out of it if he think he got beat up because he asked for a shirt.

Then Neal looked up and Peter could see panic and fear in his eyes. "Wait. No. No, I-I resisted arrest. And fought back, th - they had to hurt me. I tried to run," Neal said, looking up at Peter with pleading eyes. Like he was asking Peter to believe him. "That's what happened." Then he looked down, looking almost ashamed. "I'm sorry," he said with a sad voice. Peter was not sure what to believe.

"It's okay buddy. Helps coming. We'll get you fixed up," Peter said.

After a few more minutes of reassurances, a male and female paramedic came into the room with a gurney. "Can you tell me what we got here?" The female paramedic – her name tag said Dawson – said.

"He took a few hits and he said he hit his head. His pupils were dilated. I think he has a concussion." Peter said as he stood up and backed up a few steps.

"Pupils are definitely dilated." The male paramedic – his name tag showing him as Dunn – said as he flashed his pen light in Neal's eyes. Neal yelped in surprise and pain and pulled away, almost falling out of his chair in the process, but Peter came and held him up.

"You're okay Neal. They're here to help," Peter tried to calm him down.

"Let's get him on the gurney," Dawson said. Peter helped them move Neal to the gurney and laid him down. By the time they finished moving him, Neal was breathing quick and shallow and his eyes were pinched shut.

Dunn pulled some scissors out of his bag and cut open Neal's shirt, to see the damage. Dunn pushed down on one of the bruises on Neal's chest to see if there were any brakes, and Neal cried out in pain and tried to move away again.

Peter grabbed Neal's hand and said, "It's okay Neal there just trying to help. I'm right here. Let them help. Okay?" Neal looked at Peter with pain filled blue eyes and nodded, squeezing Peter's hand back.

Then they proceeded to strap Neal to the gurney and wheeled him out of the room and to the ambulance waiting outside, Peter never letting go of Neal's hand.


	3. Safety can only last so long

Neal

After two hours of poking and prodding, the highly paid torturers some call doctors decided that Neal was not going to die. However, they did come to the conclusion that he had two cracked ribs, a concussion and lots of bruises. And they also said that he had to stay the night for observation.

So now Neal was in the small hospital room he was going to spend the night in, wearing a pair of blue scrubs he charmed a nurse into giving him, trying – and failing – to stay awake. He knew Peter would be in here soon, he had to come up with a plan for Peter to believe him. But all Neal wanted to do was curl up in his bed and sleep for a while.

Neal was just about to fall asleep when the door opened and Brooks walked in.

Neal's heart rate picked up and Brooks could hear it from the heart monitor that Neal was hooked up to. Blasted machine. Brooks walked up to the bed. "Miss me?" he said with a smirk.

"I didn't say anything," Neal said.

"Good," he said and pulled out his cuffs. "You're still in custody. Just because Burke said he was with you doesn't mean we can just let you go. You're a criminal, you could run."

He put one cuff on the railing and the other on Neal bandaged left wrist, tightening them until they dug into Neal's skin and he winced. "Wouldn't want you escaping now would we?" Brooks said and Neal just glared. "See you later Caffery," he said and left.

Neal looked at his wrist. He couldn't slip out of the handcuffs, but he could pick them. Just to loosen them a little.

There was a pen on the table next to the bed, the left side of the bed. His left wrist was the one handcuffed. Neal didn't think he could reach his right hand and grab it without really hurting himself, so he didn't.

The door opened again and Peter came in looking solemn but trying to hide it behind a smile. "Hey Neal, how-" Peter looked down at the handcuffs then back up to Neal. "Neal, why are you cuffed?" Peter asked.

"They say I'm a flight risk," Neal said and shrugged.

"Who are 'they' Neal?" Peter asked.

"Brooks. He was in here a few minutes ago."

"Who's Brooks?"

"He's-" Neal wasn't sure what he wanted to say, or what Brooks wanted him to say, so he said, "You don't know him?"

"No. I know a Myers. He's the detective on the Downs case. Who's Brooks?"

Neal couldn't say anything about Brooks, but he couldn't lie to Peter. So he diverted. "Did you tell them you were with me Friday?"

"Yes, but..." Peter didn't seem to want to continue but he said "You weren't with me for half an hour, when you went to get something to eat. It was around the same time Downs died."

"But can't my tracker tell you where I was?" Neal hadn't meant to take that long to get food, but the first two places he tried were closed, so he had to go a few more blocks than he originally was going to.

"Your tracking data has been altered. It says you're at your apartment right now. So we can't really use that until we fix it," Peter replied sadly.

There was a somewhat awkward silence hanging over them for a few seconds. Neal moved his left hand to try to get more comfortable, but the metal dug into the bruised flesh and he winced.

Peter noticed and came closer to look at the cuffs "Are you ok?"

"Yeah, just a little uncomfortable."

"Why are these on so tight?" Peter said as he moved the cuff around. Neal winced and sucked in a sharp breath. "Sorry, sorry. Did Brooks do this?"

"He didn't want me to slip out of them. Apparently they know about my alleged skills," Neal said with a smirk.

Peter took his handcuff key again and loosed the cuff on Neal's wrist. "I think you're going to stay right here. Right?" Peter said with a pointed look.

"Right," Neal replied with a nod.

"So, you're going to tell me what happened or am I going force it out of you?" Peter said in mock sternness.

Fear flashed across Neal's face for a spit second and Peter noticed. He was about to say something, but Neal beat him to it. "They said I killed someone and I guess I freaked out. I didn't want to go to jail," Neal said while looking at his lap.

"And you fought back?"

"Yeah, I guess."

Peter went around to the right side of the bed and picked up Neal's hand. His knuckles had no marks on them. Peter looked at Neal, asking a silent question. "I didn't use my fists. I kicked one, I used my elbow and knee too."

"Okay...why did they have to knock down your door?" Peter asked as he put Neal's hand back down.

"I didn't answer the door. They think I'm a killer, there not just going to wait patiently until I let them in," Neal said then yawned.

"You look tired. I'll let you sleep. We'll talk more later," Peter patted Neal in the arm and left.

Neal let out a sigh of relief. He hated lying to Peter but he had to keep him safe. He just hoped Peter will believe him.

The next day Neal was sitting on the edge of the bed in the hospital room in jeans and a black polo shirt Peter brought from his apartment. He was waiting for Peter to come back from signing Neal out of the hospital. All Neal wanted to do was go home, but he had to go back to the station, because apparently he's still arrested. At least they haven't cuffed him again, yet.

The door opened and Mr Big and Scary from the other night and another officer came in with Peter in tow. Mr big and scary – his name tag said 'Halstead' – told the other officer to cuff him. The other officer -his name tag said Downs – Downs? Crap, that wasn't not good. Downs was not as big or scary, but still looked mean and angry. He was maybe 30 years old or so and the dead Downs had looked about the same age. Brothers maybe? Neal stood up and Downs came over a cuffed Neal's hands behind his back, but not that tightly. Maybe they don't want to be mean in front of the federal agent.

"We'll figure this out Neal," Peter said to Neal as he passed.

"I know we will Peter," But Neal's wasn't sure what it was that Peter could do.

Halstead and Downs took Neal out to the parking lot and put him in the back seat of the cruiser and drove off to the station.


	4. Not The Station

Peter

Peter was not happy about any of this. He could tell that Neal was not telling him everything, he just didn't know what. In all the time he had known the con man he had gotten quite good at detecting evasion tactics, at noticing the not really lies. He knew Neal was hiding something, he just couldn't figure out what it was.

He had seen the fear that had flashed across his CI's face when the officers came and got him. Maybe it had just been the fear of being arrested again. But no matter how much he tried, Peter couldn't shake off the feeling that it was something more.

No matter what Neal was hiding, he wouldn't kill anyone. Neal was a lot of things, but he wasn't a murderer. That was the only thing Peter was sure of right now.

He tried telling them that but the officers were not really in the mood to listen. Neal's tracking data was still messed up.

And it didn't make sense that Neal would resist arrest. Peter had always known him to shirk away from any kind of violence, he was the most passive person Peter knew. Peter had also looked up Brooks' file and a lot of the people he had arrested over the years seemed to resist arrest and get themselves beaten up a little bit.

Something wasn't adding up. And Peter was going to figure it out.

Peter got in his car and made his way to the station.

Neal

Halstead and Downs didn't say a word as they drove to the station. It was a little nerve racking.  
>But as they approached the station Halstead didn't slow down and drove past it. "Uh guys? I think you missed the station," Neal said. They drove another block and turned into an alley. There was an SUV parked there. Halstead parked the car next to the SUV and turned off the engine. Halstead and Downs got out and Downs opened the back door and pulled Neal out, tightening the cuffs. Downs held one of Neal's arms and Halstead held the other.<p>

"This doesn't look like the station," Neal said as he was brought to the SUV. The back door opened and Brooks came out. Not him again. "Didn't say anything to anyone," he told Brooks.

He walked up to Neal and growled, "Then why did your fed friend look me up?"

"Peter? I didn't say anything. He probably just looked you up to see your arrest record or something."

"How does he even know my name?"

"Umm..." And wasn't that the smartest that he could say.

"You told him my name!?" Brooks yelled and held his fist up.

"Wait, wait! I didn't mean to! It just slipped out!" Neal cried, trying to pull back, but Downs and Halstead were holding him.

"Oh, well if it just slipped out," Brooks said smirking, and punched Neal in the stomach. Neal coughed and winced from him hitting the same spot as before. "I warned you not to say anything," Brooks told Neal, punching him again.

He held his fist up again, about to punch Neal again "Wait!" Neal said and Brooks actually stopped. "How are you going to explain my new injures? Couldn't you get in trouble for attacking an unarmed man?"

Brooks shrugged. "You tried to get away. We were forced to subdue you," he said with an evil grin and punched Neal in the face.

Neal glared at him and spit blood out of his mouth, "I think this is police brutality."

Brooks grabbed Neal's hair and whispered, "Not if we say it isn't." He let go of his hair and punched him in the chest. Neal groaned as the breath was knocked out of him.

Neal thought that he should bring some humour to the situation. "You hit like a girl."

By the look on Brooks face, he did not think it was funny. "Let him go," he told the officers holding him. Downs and Halstead let go of Neal. He thought of running but he knew all three men were armed and he didn't want to get shot in the back. "How about we see if I kick like a girl."

"I personally don't know what that feels like."

"Oh well," Brooks said, then grabbed Neal's shoulders and brought Neal's chest down to his lifted knee, then let go of him. Neal dropped to his knees, gasping for air.

"That wasn't your foot, it was your knee," he commented when he got some of his air back.

"Oh, sorry," Brooks replied sarcastically. He kicked Neal in the stomach then pushed him to his side. Neal couldn't resist, he was just trying to control the pain that seemed to be everywhere. "Is that better?"

"Much," Neal said, breathless.

After Neal was down it seemed like fair game to all three of them. Kick after kick hit Neal in the chest, stomach, back, and legs. His hand were cuffed behind his back so he couldn't even try to defend himself. The pain was all that seemed to exist.

A few of the blows hit him in the head and Neal's vision was going black around the edges when he heard shouting. He couldn't hear what they were saying but the kicks stopped, so he mentally thanked the voice right before he passed out.


	5. Safety Finding Neal Again

Peter

After asking the lady at the front desk of the police station and looking around himself, Peter couldn't find Neal.

So he got back in his car and was driving down the road, about to turn around when he saw a police car and an SUV in an alley. There were some people huddled around something on the ground.

Peter turned down the alley and he saw that it was a _someone_ not a something on the ground. His heart seemed to stop at the realization. Stopping the car, Peter got out, pulled out his gun and ran up to the group that was kicking someone Peter hoped against hope was not his CI.

"FBI! Back away from him, now!" He yelled as he pointed his gun at them. Anger narrowed his vision when he saw it was indeed Neal on the ground, curled up and whimpering with eyes closed tightly. Peter forced himself to look back at the other three. He saw that they were the two officers that took Neal away earlier at the hospital and another man whom he didn't recognize. They all stopped kicking Neal and backed away, with their hands in the air.

"Take out your guns and toss them here, slowly," Peter ordered. Peter wanted desperately to check on Neal, but he knew that he had to deal with them first.

"He tried to run. We were just-" the one that had a name tag that said his name was Downs – Downs? Crap – said.

Peter stopped him from saying anything else, "Shut up and do as I say."

All three of them took out there guns and two of them tossed them to Peter, but the one he didn't recognize pointed his gun at Peter. Peter fired before he could get a shot off. The bullet hit him right in the shoulder and he fell to the ground.

Peter pulled out his handcuffs and threw them to the angrier looking one and said, "Put those on him." Motioning to the man on the ground. He obeyed Peter's order. "Now take out your handcuffs and cuffs yourselves to the car," Peter instructed.  
>Now that they were taken care of, Peter ran over to Neal, who hadn't moved yet, while calling 9-1-1 and telling them where they were, what had happened, and that they needed to come now. He also called Diana to tell her to get down as fast as she could. He didn't trust the police to handle the situation.<p>

He kneeled down next to his partner who was on his side with his eyes closed.  
>Peter took a look at Neal's still form. There was blood going down the side of his face from a cut by his hairline, and there were bruises forming all over his face. His clothes were dirty with dirt and blood, and his hands were tied behind his back.<p>

Okay first things first, pulse. Peter reached out and felt for a pulse on Neal's neck. Yes, he had one. Okay now breathing. Peter put his ear next to Neal's mouth. He was breathing, but there was a slight wheezing sound coming from the younger man.

Peter pulled out his handcuff key and unlocked the cuffs. He then carefully turned Neal so he was on his back. As he was moved, Neal moaned and squeezed his eyes shut.

"Neal buddy? You with me?" Peter asked softly as he brushed away the hair that had fallen in Neal's face.

"Peter?" Neal said in a pained voice.

"Can you open your eyes for me?" Peter asked.

Slowly Neal's eyes fluttered open and it was obvious he was fighting to stay awake. "Ow."

Peter smiled just a little. "Yeah, I'd say that about sums it up."  
>Neal nodded a little and his eyes started to close. "No, none of that. Come on, open up."<p>

Neal moaned and reluctantly obeyed. Blue eyes looked up at the agent and he could see fear in them. "Are they gone?" Neal asked quietly.

Peter grabbed Neal's hand, careful of his wrist. "I got them. They aren't going to hurt you anymore," Peter assured him and looked over his shoulder to make sure they were where they had been when he had left them.

Neal sighed in relief and instantly regretted it, wincing as his ribs protested against the movement. He squeezed Peter's hand, riding out the pain.

"Hey, you okay?" Peter asked, not knowing what else to say. Of course he wasn't okay.

"Yup. All good. Could use some ibuprofen though," Neal quipped up, but his weak voice lacked any sign of humour and Peter could see that he was having trouble just staying awake.

"Help is coming, they'll give you the good stuff." Just as Peter said it, they could hear sirens in the distance. "See, told you." Peter said, smiling a little.

"Can I… close my eyes now?" Neal asked, looking up at Peter, pleading at him to say yes.

It broke Peter's heart to see Neal like this, "Sorry kid, just a little longer, okay? Then you can sleep."

Neal didn't say anything but managed to give Peter a brief smile.

Then finally the ambulance pulled into the alley, as did three SUV's that Peter knew held the FBI agents he also called. Two paramedics jumped out of the ambulance and made their way to the duo.

"What have we got?" The male paramedic – Peter read his name tag, it said Jackson – said.

"I wasn't here for it all but when I did arrive, those three-" he pointed to the two policemen and the detective that were being arrested by Jones, Diana, and two other agents. "were beating him up and he was unconscious," Peter stood and backed up to give them space to work.

"What's his name?" Jackson asked as he got an IV ready.

"Neal," Peter and Neal said in unison.

"Okay Neal, where does it hurt?" The female paramedic – her name tag said Morgan – asked as she cut open Neal's black polo shirt and couldn't hide a wince of sympathy. Neal's chest and stomach looked even worse than it did yesterday. He could see the older bruises were dark blue and purple, but the new ones were an angry red. They had to hurt.

"Chest, head, back, wrists, everywhere really. It hurts to breathe," Neal said sleepily.

Jackson then put an oxygen mask over Neal's face. "Okay, we're going to put you on to the gurney, okay?" Jackson said as he positioned himself.

"M'kay," Neal said his voice muffled by the mask, not really interested in what they were saying anymore.

The two paramedics and Peter lifted Neal onto the gurney and wheeled him to the back of the ambulance. Peter and Jackson jumped in the back with Neal and while Morgan went to the driver's seat and started up the vehicle.

Neal looked around, panicked, as if searching for something- no someone, and his hand was gripping the bed like a substitute for whom he wanted to hold on to. Peter wasted no time in getting into the ambulance and taking Neal's hand in his own. He squeezed it a little. "I'm right here, kid."

Neal looked at him with half lidded eyes. "Can I close my eyes now?" He asked with the same look as before, albeit sleepier.

Peter looked to Jackson for conformation, and when he nodded Peter looked back at Neal and said with a small smile, "Yeah buddy. You can rest now." He smiled when Neal obeyed instantly.

Once he know Neal was asleep, Peter asked "Is he going to be okay?"

Jackson looked to the sleeping form on the gurney. He didn't look good. "He has substantial bruising to the torso, and that makes me concerned about internal bleeding," The look on Peter's face made him rush onwards to calm the man. "But we won't know until we get to the hospital, it could just be some cracked ribs." Peter nodded numbly.

"What else?"

Jackson worked on Neal while he explained. "Well, he seems to be having some trouble breathing, so the cracked, or possibly broken ribs could be pressing on his lungs, but if they were punctured, we would know by now," Jackson said, now wanting to tell him that Neal wouldn't be able to breathe if that was so, but by the look of the guy, he knew.

Peter squeezed Neal's hand a little harder, making sure he knew he was here, not letting go until they arrived at the hospital.


	6. Back To The Hospital

1h agoNeal

Neal woke to an annoying beeping sound. He wished it would stop being so loud, it was making his head hurt. He shifted and his body came alive with pain and the annoying beeping sped up, making it even more annoying. He moaned and squeezed his eyes shut, waiting for the pain to die down to a distant throb that only seemed to only be possible in his state from lots of painkillers.

"Neal? You awake?" A voice from his left that sounded a lot like Peter said.

"Mm, no," Neal replied in a thick voice.

"Oh, okay. I guess you don't get jello then."

"Jello? What flavor?" Neal asked, interested in the idea of eating.

"You'll have to open your eyes to find out," the Peter like voice said, teasingly.

"Fine." Neal said and slowly opened his eyes, looking to the left and seeing the Peter like voice belonged to someone that looked like Peter. Neal slowly came to the conclusion that the Peter like person was in fact Peter. He must be on some good drugs. Neal looked around for the jello, but couldn't see any. He frowned and said "Jello?" Looking up at Peter with pleading eyes.

Peter rolled his eyes and brought four jello cups seemingly out of nowhere. "I got cherry, strawberry, grape, and pineapple. Which one do you want?"

After a second of thinking he said, "Strawberry please." With a grateful smile.

Peter put the other three cups down and gave Neal the strawberry flavored one with a spoon. Neal took the offered items, taking a spoonful of yummy jello. After a few bites, Neal's eyes started to droop. Not a minute later he was asleep.

Peter

Peter couldn't help but smile at the sight of Neal. He fell asleep with his spoon still in his mouth and the cup of jello in his limp hand, about to fall off the bed. He looked like a small child that missed his nap and fell asleep during snack time. Peter took the cup out of the younger man's hand and grabbed the spoon, putting them in the trash.

Peter took another look at the young man in the bed. He looked better than he did in the alley, but the bruises on his face were much darker than they were yesterday. The blood from the cut on the side of his head was cleaned and stitched up, and was a nasal canal under his nose, giving him oxygen. He couldn't see the bruises covering Neal's torso, but he knew they were there. But all that seemed to matter was that he was going to be okay.

Peter picked up the two month old magazine he was reading and waited for Neal to wake up again. He was not going to leave him alone for a long time.

Neal

The next time Neal woke up he seemed to actually be able to put two thoughts together. But with his head a little more clear, he could feel a lot more of the damage that was done to his body. 'They must have taken me off the good stuff.' Neal thought, and opened his eyes. He looked to his left and saw Peter in what could only be described as the most uncomfortable position he could have gotten himself in. His head was tilted back with his mouth open, and was making strange snoring sounds that made Neal smile. His arms and legs were a twisted mess that made Neal wonder how that had happened.

Neal knew that he had to wake up his friend, but how? Neal looked around and saw a bag of popcorn on the night stand.

A mischievous smile formed on Neal's face as he got an idea.

Neal grabbed the bag off the table, careful of his injures, and got a piece out then threw it at his partner. It missed by about a foot and hit the floor.

He got out another and tried again. This time his aim was true, hitting Peter in the chest, but the agent slept on, not noticing the attack. Neal hit him four more times, but he didn't even stir.

Getting frustrated, Neal sat up more, grabbed a big handful and trust the popcorn at Peter as hard as he could. It woke his many injuries, but Peter startled awake, looking around, first at Neal then at the popcorn that was all over Peter and the floor, then back at Neal, who was grinning at Peter like he just won a game at the fair he tried forever to win, his prize, of course, was to see his friend awake. "Hey."

"Why am I covered with popcorn?" Peter asked, more confused than angry.

"Someone had to get you out of that position you got yourself in somehow," Neal said with shrugged and winced.

Peter just shook his head and brush off the popcorn to the floor.

"Can I have some water?" Neal asked after a second.

"Yeah. Sure," Peter said left to fill up a cup in the bathroom. He came back with the cup and a straw. Neal took the offered items gratefully, taking a sip of the cool liquid. He gave the cup back to Peter and asked, "no cuffs?" While moving his hands around.

"I convinced them that you weren't going anywhere. but... They still think you killed Downs." Peter said apologetically.

"Oh." Neal said. They will have still have to deal with the false charges, but Neal knew Peter would do all he could to help. "What's the damage?" Neal asked quietly.

Peter sighed and sat down, leaned forward, putting his elbows on his knees and interlocking his fingers. "You have a concussion, three broken ribs, two cracked ones, and lots of bruises on your face, chest, stomach, and wrists," Peter said, looking angrier by the second.

"It's not your fault, Peter." Neal said, guessing what Peter might be thinking.

Peter thought about that for a second. "What happened?" Peter said looking right in the eyes.

"What do you know?" Neal asked slowly.

"Just spit it out Neal. They're locked up. They can't hurt you anymore."

"It's not me I'm worried about," Neal muttered.

"What did you say?" Peter asked.

"Are you sure they'll stay there?"

"Yes. They were kicking you while you were on the ground with your hands already cuffed. You were defenceless, Neal."

Neal sighed then winced. "They thought that I killed a police officer."

"I know that."

"Well you didn't let me finish."

Peter leaned back in his chair and signalled Neal to continue. "They were mad because they thought I killed Downs so they roughed me up. I'm sure you'd be mad if jones or Diana were killed."

Peter did not seem happy that Neal was making excuses for the b***. "I want names," Peter said going all FBI agent on Neal.

"Brooks, Downs and Halstead."

"So you didn't resist?" Peter asked. Neal shook his head. "Or fight back?"

"No." Neal looked away, ashamed for lying to Peter.

"Why didn't you just tell me?" Peter asked, confused that Neal didn't come to him for help.

Neal looked up at Peter hesitantly and said, "Brooks threatened you."

Peter was taken aback slightly. He knew that Neal trusted and liked Peter, but to take a beating for him? That was farther than he thought the ex con would go. "Oh," Peter said eventually.

After a few seconds of awkward silence Neal said "So when can I get out of here?"

"Tomorrow maybe," And Neal's face fell, but then he smiled a little and looked like he was planing something. "No jail brakes. You need to stay here and get better," Peter said, pointing a finger at Neal.

"Of course not," Neal said we with a big smile, but it was interrupted by a yawn.

"You should get some rest," Peter said getting up.

"You're leaving?" Neal asked quietly.

Peter stopped in his tracks. "You want me to stay?"

Neal said "You don't have to. I'm sure El's waiting for you." But he wanted to say, 'Yes, please don't go.'

"I was just going to get some coffee, but it can wait." Peter said sitting back down with a smile.

Neal smiled back and fell into a restful sleep, knowing that Peter was there to keep him safe.


	7. At the office

**Hello**** people! I know it's been a while, I haven't had any inspiration for this story so I've been working on my other story's. Anyway, enjoy!**

The next day Neal was released from the hospital and Peter helped him to the car. Moving or breathing was quite painful, but the pills the doctor had given him helped dull the pain.

After a few minutes of driving, Neal realized where they were going. "Are we going to the office?"

Peter had an apologetic look on his face. "The anklet is still not working. Hughes said you can't just go home. I'm sorry," he said the last part quietly.

"So you need to keep me close enough to watch me," Neal elaborated. "Are you going to have to lock me up or handcuff me or something?" he asked, his voice subdued.

"No, no. We just have to keep you at the office until the tracker's fixed," Peter said, visibly upset at the thought of Neal locked up again. The last time had probably been hard on him too Neal guessed. "Jones got some clothes from your apartment. The doors still not fixed anyway."

"Can we send the department the bill?" Neal said, only half joking.

"No, you didn't answer the door. That's not their fault."

"Well it was late, and I was tired," Neal said as if that explained everything.

They finally made it to the office and they slowly made their way to the 21st floor, mindful of Neal's injures. By the time Neal was sitting down across from Peter in his office he had a thin layer of sweat on his face and he was breathing heavily. The pain was much worse than when he was in the car, but now that he was sitting again, he was starting to feel a little better.

"You okay?" Peter noticed Neal's pained look, but knew Neal would deny it. He was hoping that if Neal needed to stop he would say so.

"Yeah, just need a minute," Neal said, wrapping an arm around his middle protectively.

After a few minutes of Neal's deep breathing and Peter pretending to look at a file while watching Neal, Neal looked up at Peter and nodded, silently telling him that he was okay, and the ambulance that he was surely thinking about calling was not necessary.

"Whenever you're ready, I or another agent can take your statement." Peter had that apologetic look on his face again, as if he thought it was his fault. But Neal knew it wasn't.

"I'm ready. And could you take my statement?" Neal didn't want to give his statement at all, but Peter being there may make it bearable.

"Yeah," Peter said maybe a little too fast. "Let me just get some stuff," he said as he got up and left the office, patting Neal's shoulder as he passed.

Peter came back with recording equipment and set it up on the desk between them. "Start whenever you're ready," Peter said.

Neal proceeded to tell Peter, and the microphone about the events of the last few days. It took a few hours and by the time they were finished Neal was tired, hungry and in need of more pain medication.

As Peter was picking up the equipment Jones knocked on the door. "Hey Peter, Neal," he said, nodding at each of them. "I got some food from the deli down the street, thought you guys might want some," he handed Neal a sandwich and offered Peter one.

"Thanks Jones, but I'm going to talk to Hughes for a minute," Peter said as he finished picking up the equipment and walked out of his office, while Neal dug into his sub, wondering what Peter was going to talk to his boss about.

Forty-five minutes later Peter walked back into his office looking for Neal, but he wasn't in the seat he had been in when he left, he was lying on the small couch, curled up on his side, sleeping, looking to all the world like an innocent young man, but Peter knew better. 'Though this time he was actually innocent,' Peter reminded himself. 'The kid always seems to find trouble, even when he's not looking for it.'

Peter didn't want to wake Neal up but he knew he had to. "Neal," Peter said as he gently shook the younger man's shoulder. Neal moaned and opened his eyes. "Hey, you awake?"

He looked up at Peter and said "Mm, yeah. I haven't gotten much sleep recently." Peter nodded in agreement, His anger flaring up again at the ones responsible for Neal's lack of sleep. "What did you go talk to Hughes about?"

The question brought Peter out of his thought and back to the matter at hand. Neal sat up and moved his legs off the couch so Peter could sit next to him. Peter sat down and said "Hughes wanted you to stay here until the tracker was fixed."

"Yeah I know that, you told me."

"Yes, but you didn't let me finish," Peter said with a small smile on his face, remembering their conversation from last night when their roles had been switched. Neal seemed to remember as well. He had a smile on his face as well and motioned Peter to continue just like Peter did the night before.

"The Marshals won't have a new anklet for a few days and I told Hughes you can't stay here that long." A flash of fear came across Neal's face at those word and for a second Peter was confused, but quickly understood. "I'm not sending you to jail," Peter reassured. The fear was replaced by confusion, so Peter continued. "You're going to stay with me and El for a little while." If anything that made Neal look even more confused.

"Are you sure? I don't want to be any trouble, I can just stay here."

"You're always trouble, no matter where you go," Peter half joked, but continued in a no-nonsense tone. "But no, you're coming home with me and that's final."

Neal seemed to consider this for a moment, then said "well your couch at your house is more comfortable that this one," while glaring at the offending object as if it was to blame for all the pain he was in. "Wait, Hughes is allowing this?" Neal asked.

Peter smiled. "He did eventually." Neal smiled back, silently thanking Peter for getting their boss to agree to let him stay at the Burkes, where he knew that he would be more comfortable.

**thank you for reading! Reviews make me smile!**


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